Papers by Marie Ndjiondjop
Plants, 2021
The inherent ability of seeds (orthodox, intermediate, and recalcitrant seeds and vegetative prop... more The inherent ability of seeds (orthodox, intermediate, and recalcitrant seeds and vegetative propagules) to serve as carriers of pests and pathogens (hereafter referred to as pests) and the risk of transboundary spread along with the seed movement present a high-risk factor for international germplasm distribution activities. Quarantine and phytosanitary procedures have been established by many countries around the world to minimize seed-borne pest spread by screening export and import consignments of germplasm. The effectiveness of these time-consuming and cost-intensive procedures depends on the knowledge of pest distribution, availability of diagnostic tools for seed health testing, qualified operators, procedures for inspection, and seed phytosanitation. This review describes a unique multidisciplinary approach used by the CGIAR Germplasm Health Units (GHUs) in ensuring phytosanitary protection for the safe conservation and global movement of germplasm from the 11 CGIAR genebank...
Plants, 2020
The international collections of plant genetic resources for food and agriculture (PGRFA) hosted ... more The international collections of plant genetic resources for food and agriculture (PGRFA) hosted by 11 CGIAR Centers are important components of the United Nations Food and Agriculture Organization’s global system of conservation and use of PGRFA. They also play an important supportive role in realizing Target 2.5 of the Sustainable Development Goals. This paper analyzes CGIAR genebanks’ trends in acquiring and distributing PGRFA over the last 35 years, with a particular focus on the last decade. The paper highlights a number of factors influencing the Centers’ acquisition of new PGRFA to include in the international collections, including increased capacity to analyze gaps in those collections and precisely target new collecting missions, availability of financial resources, and the state of international and national access and benefit-sharing laws and phytosanitary regulations. Factors contributing to Centers’ distributions of PGRFA included the extent of accession-level informat...
Scientific Reports, 2021
Morphological identification of closely related rice species, particularly those in the Oryza AA ... more Morphological identification of closely related rice species, particularly those in the Oryza AA genome group, presents major challenges and often results in cases of misidentification. Recent work by this group identified diagnostic single nucleotide polymorphic (SNP) markers specific for several rice species and subspecies based on DArTseq next-generation sequencing technology (“DArTseq”). These SNPs can be used for quality control (QC) analysis in rice breeding and germplasm maintenance programs. Here, we present the DArTseq-based diagnostic SNPs converted into Kompetitive allele-specific PCR (KASPar or KASP) assays and validation data for a subset of them; these can be used for low-cost routine genotyping quality control (QC) analysis. Of the 224 species/subspecies’ diagnostic SNPs tested, 158 of them produced working KASP assays, a conversion success rate of 70%. Two validation experiments were run with 87 of the 158 SNP markers to ensure that the assays amplified, were polymor...
Compendium of Plant Genomes, 2018
Oryza glaberrima is the African cultivated rice species, domesticated from its wild ancestor by f... more Oryza glaberrima is the African cultivated rice species, domesticated from its wild ancestor by farmers living in Inland Delta of Niger River. Several studies indicated that it has extremely narrow genetic diversity compared to both its wild progenitor, Oryza barthii and the Asian rice, Oryza sativa which can mainly be attributed to a severe domestication bottleneck. Despite its scarcity in farmer’s field due to its low yield potential, high shattering and lodging susceptibility, O. glaberrima is of great value not only to Africa but also globally. Perhaps its greatest contribution to regional and global food security is as a source of genes, as it possesses resistance/tolerance to various biotic and abiotic stresses. It also has unique starch-related traits which give it good cooking and eating properties. Advances in DNA sequencing have provided useful genomic resources for African rice, key among them being whole genome sequences. Genomic tools are enabling greater understanding of the useful functional diversity found in this species. These advances have potential of addressing some of the undesirable attributes found in this species which have led to its continued replacement by Asian rice. Development of new generation of rice varieties for African farmers will therefore require the adoption of advanced molecular breeding tools as these will allow efficient utilization of the wealth and resilience found in African rice in rice improvement.
Le riz cultive en altitude et en conditions hydromorphiques en Afrique de l'Ouest est soumis ... more Le riz cultive en altitude et en conditions hydromorphiques en Afrique de l'Ouest est soumis a diverses periodes et intensites de secheresse, responsable de perte de rendement. Une strategie d'amelioration varietale pour la resistance a la secheresse est developpee par l'Association pour le Developpement du Riz en Afrique de l'Ouest. La selection recurrente est utilisee pour elever le niveau de resistance dans le germplasm de Oryza sativa et de O. glaberrima identifie comme tolerant. Des croisements entre ces 2 especes ont pu etre realises de facon satisfaisante. La culture d'antheres des F1 et F2 de ces croisements interspecifiques ameliore le niveau de fertilite et accelere l'obtention de lignees homozygotes. Ces descendances montrent une certaine resistance aux stades vegetatif et reproductif
African Journal of Biotechnology, 2006
The Africa Rice Center (WARDA) has developed several interspecific rice varieties by crossing the... more The Africa Rice Center (WARDA) has developed several interspecific rice varieties by crossing the high yielding Asian rice (Oryza sativa subsp. japonica) with the locally adapted African rice (Oryza glaberrima). Eighteen varieties were named with the prefix NERICA (New Rice for Africa) but their genetic difference and patterns of relationship is largely unknown. A total of 102 polymorphic microsatellite markers were used to genotype 18 NERICAs. A subset of seven NERICAs (NERICA 1 to 7) was further characterized for 10 agronomic traits. The microsatellites data revealed no genetic difference between NERICA 8 and 9. The absence of genetic distance and identical SSR haplotype distribution (banding pattern) observed between NERICAs 8 and 9 is highly likely to be due to lack molecular difference at the DNA level but the possibility for seed admixture remains to be explored. This study, however, revealed the presence of a wide range of genetic differences among all other NERICAs, with the...
Domestication represents a unique opportunity to study the evolutionary process. The elimination ... more Domestication represents a unique opportunity to study the evolutionary process. The elimination of seed dispersal traits was a key step in the evolution of cereal crops under domestication. Here, we show that ObSH3, a YABBY transcription factor, is required for the development of the seed abscission layer. Moreover, selecting a genomic segment deletion containing SH3 resulted in the loss of seed dispersal in populations of African cultivated rice (Oryza glaberrima Steud.). Functional characterization of SH3 and SH4 (another gene controlling seed shattering on chromosome 4) revealed that multiple genes can lead to a spectrum of non-shattering phenotypes, affecting other traits such as ease of threshing that may be important to tune across different agroecologies and postharvest practices. The molecular evolution analyses of SH3 and SH4 in a panel of 93 landraces provided unprecedented geographical detail of the domestication history of African rice, tracing multiple dispersals from a core heartland and introgression from local wild rice. The cloning of ObSH3 not only provides new insights into a critical crop domestication process but also adds to the body of knowledge on the molecular mechanism of seed dispersal
Oryza longistaminata is a distantly related wild rice relative found only in Africa. It is agrono... more Oryza longistaminata is a distantly related wild rice relative found only in Africa. It is agronomically inferior to cultivated rice but possesses several latent useful traits that can be used to improve agronomically important traits in cultivated rice. These useful traits include strong rhizomes, a vigorous biomass, drought avoidance mechanisms, good weed suppression ability via allelopathy, and high nitrogen-use efficiency. It also possesses resistance to several biotic stresses such as brown plant hopper, nematodes, yellow stem borer, rice tungro bacilliform virus, blast, and bacterial blight. Recent studies have revealed that it is a good source of new alleles that can be used to improve yield-related traits in cultivated rice varieties. However, this potential is not well studied and is therefore not optimally exploited. Advances in genomics such as the release of whole genome reference sequence are offering opportunities for enhanced use of this species and its genetic resour...
Compendium of Plant Genomes, 2018
Despite being highly studied, the evolutionary relationships in the Oryza genus have remained inc... more Despite being highly studied, the evolutionary relationships in the Oryza genus have remained inconsistent and inconclusive. The origin and domestication history of Asian rice has particularly remained contentious. This chapter discusses the evolutionary relationships between various species in the Oryza genus, with a special focus on the application of current advances in genomics in understanding the various evolutionary dynamics. Advances in genomics are offering opportunities for resolving the origin of cultivated rice and clarifying phylogenetic and evolutionary relationships between the various Oryza species. Analysis of genomes of cultivated rice and their putative progenitors is providing useful information such as unusually diverged genomic regions, which provides vital insights into rice evolution, domestication and demographic history. However, with the increase in whole genome sequence data, it appears that data analysis and subsequent interpretation may now present the next challenge in efforts aimed at resolving this hot debate. The use of nuclear and whole chloroplast genome sequences is helping define the relationships between the recent newly discovered Australian taxa which are believed to be novel gene pools. In this chapter, we have also discussed the challenges faced in efforts aimed at resolving evolutionary relationships in the Oryza genus.
Plants, 2020
Asian and African rice gene pools vary in many traits that are important in rice breeding. The ge... more Asian and African rice gene pools vary in many traits that are important in rice breeding. The genetic basis of these differences was evaluated by analysis of important agronomic traits in crosses between African and Asian rice. Trait-associated variants (TAVs) influencing three quantitative agronomic traits, heading date (Hd), tiller number at maturity (T), and 1000 grain weight (TGW), were identified by association analysis of crosses between Asian and African rice. Populations were developed by crossing WAB56-104 (Oryza sativa) and CG14 (Oryza glaberrima). DNA from plants with extremely high or low values for these phenotypes was bulked and sequenced. The reference genome of O. sativa cv Nipponbare was used in general association analysis and candidate gene analysis. A total of 5152 non-synonymous single nucleotide polymorphisms (SNPs) across 3564 genes distinguished the low and the high bulks for Hd, T, and TGW traits; 611 non-synonymous SNPs across 447 genes were found in KEGG ...
Plants, 2019
African rice (Oryza glaberrima) has a pool of genes for resistance to diverse biotic and abiotic ... more African rice (Oryza glaberrima) has a pool of genes for resistance to diverse biotic and abiotic stresses, making it an important genetic resource for rice improvement. African rice has potential for breeding for climate resilience and adapting rice cultivation to climate change. Over the last decade, there have been tremendous technological and analytical advances in genomics that have dramatically altered the landscape of rice research. Here we review the remarkable advances in knowledge that have been witnessed in the last few years in the area of genetics and genomics of African rice. Advances in cheap DNA sequencing technologies have fuelled development of numerous genomic and transcriptomic resources. Genomics has been pivotal in elucidating the genetic architecture of important traits thereby providing a basis for unlocking important trait variation. Whole genome re-sequencing studies have provided great insights on the domestication process, though key studies continue givin...
Nature plants, 2018
Domestication represents a unique opportunity to study the evolutionary process. The elimination ... more Domestication represents a unique opportunity to study the evolutionary process. The elimination of seed dispersal traits was a key step in the evolution of cereal crops under domestication. Here, we show that ObSH3, a YABBY transcription factor, is required for the development of the seed abscission layer. Moreover, selecting a genomic segment deletion containing SH3 resulted in the loss of seed dispersal in populations of African cultivated rice (Oryza glaberrima Steud.). Functional characterization of SH3 and SH4 (another gene controlling seed shattering on chromosome 4) revealed that multiple genes can lead to a spectrum of non-shattering phenotypes, affecting other traits such as ease of threshing that may be important to tune across different agroecologies and postharvest practices. The molecular evolution analyses of SH3 and SH4 in a panel of 93 landraces provided unprecedented geographical detail of the domestication history of African rice, tracing multiple dispersals from ...
Molecular Breeding, 2018
Species misclassification (misidentification) and handling errors have been frequently reported i... more Species misclassification (misidentification) and handling errors have been frequently reported in various plant species conserved at diverse gene banks, which could restrict use of germplasm for correct purpose. The objectives of the present study were to (i) d e t e r m i n e t h e e x t e n t o f g e n o t y p i n g e r r o r (reproducibility) on DArTseq-based single-nucleotide polymorphisms (SNPs); (ii) determine the proportion of misclassified accessions across 3134 samples representing three African rice species complex (Oryza glaberrima, O. barthii, and O. longistaminata) and an Asian rice (O. sativa), which are conserved at the AfricaRice gene bank; and (iii) develop species-and sub-species (ecotype)-specific diagnostic SNP markers for rapid and low-cost quality control (QC) analysis. Genotyping error estimated from 15 accessions, each replicated from 2 to 16 times, varied from 0.2 to 3.1%, with an overall average of 0.8%. Using a total of 3134 accessions genotyped with 31,739 SNPs, the proportion of misclassified samples was 3.1% (97 of the 3134 accessions). Excluding the 97 misclassified accessions, we identified a total of 332 diagnostic SNPs that clearly discriminated the three indigenous African species complex from Asian rice (156 SNPs), O. longistaminata accessions from both O. barthii and O. glaberrima (131 SNPs), and O. sativa spp. indica from O. sativa spp. japonica (45 SNPs). Using chromosomal position, minor allele frequency, and polymorphic information content as selection criteria, we recommended a subset of 24 to 36 of the 332 diagnostic SNPs for routine QC genotyping, which would be highly useful in determining the genetic identity of each species and correct human errors during routine gene bank operations.
Current biology : CB, Jan 23, 2018
African rice (Oryza glaberrima) was domesticated independently from Asian rice. The geographical ... more African rice (Oryza glaberrima) was domesticated independently from Asian rice. The geographical origin of its domestication remains elusive. Using 246 new whole-genome sequences, we inferred the cradle of its domestication to be in the Inner Niger Delta. Domestication was preceded by a sharp decline of most wild populations that started more than 10,000 years ago. The wild population collapse occurred during the drying of the Sahara. This finding supports the hypothesis that depletion of wild resources in the Sahara triggered African rice domestication. African rice cultivation strongly expanded 2,000 years ago. During the last 5 centuries, a sharp decline of its cultivation coincided with the introduction of Asian rice in Africa. A gene, PROG1, associated with an erect plant architecture phenotype, showed convergent selection in two rice cultivated species, Oryza glaberrima from Africa and Oryza sativa from Asia. In contrast, a shattering gene, SH5, showed selection signature duri...
Briefings in functional genomics, 2018
Global efforts have seen the world's plant genetic resources (PGRs) conserved in about 1625 g... more Global efforts have seen the world's plant genetic resources (PGRs) conserved in about 1625 germ plasm repositories. Utility of these resources is important in increasing the resilience and productivity of agricultural production systems. However, despite their importance, utility of these resources has been poor. This article reviews the real and potential application of the current advances in genomic technologies in improving the utilization of these resources. The actual and potential application of these genomic approaches in plant identification, phylogenetic analysis, analysing the genetic value of germ plasm, facilitating germ plasm selection in genebanks as well as instilling confidence in international germ plasm exchange system is discussed. We note that if genebanks are to benefit from this genomic revolution, there is need for fundamental changes in the way genebanks are managed, perceived, organized and funded. Increased collaboration between genebank managers and ...
Genome biology and evolution, 2017
Oryza glaberrima is one of the two cultivated species of rice, and harbors various interesting ag... more Oryza glaberrima is one of the two cultivated species of rice, and harbors various interesting agronomic traits, especially in biotic and abiotic resistance, compared with its Asian cousin O. sativa. A previous reference genome was published but newer studies highlighted some missing parts. Moreover, global species diversity is known nowadays to be represented by more than one single individual. For that purpose, we sequenced, assembled and annotated de novo three different cultivars from O. glaberrima. After validating our assemblies, we were able to better solve complex regions than the previous assembly and to provide a first insight in pan-genomic divergence between individuals. The three assemblies shown large common regions, but almost 25% of the genome present collinearity breakpoints or are even individual specific.
PloS one, 2016
African rice gall midge (AfRGM) is one of the most destructive pests of irrigated and lowland Afr... more African rice gall midge (AfRGM) is one of the most destructive pests of irrigated and lowland African ecologies. This study aimed to identify the quantitative trait loci (QTL) associated with AfRGM pest incidence and resistance in three independent bi-parental rice populations (ITA306xBW348-1, ITA306xTOG7106 and ITA306xTOS14519), and to conduct meta QTL (mQTL) analysis to explore whether any genomic regions are conserved across different genetic backgrounds. Composite interval mapping (CIM) conducted on the three populations independently uncovered a total of 28 QTLs associated with pest incidence (12) and pest severity (16). The number of QTLs per population associated with AfRGM resistance varied from three in the ITA306xBW348-1 population to eight in the ITA306xTOG7106 population. Each QTL individually explained 1.3 to 34.1% of the phenotypic variance. The major genomic region for AfRGM resistance had a LOD score and R2 of 60.0 and 34.1% respectively, and mapped at 111 cM on chro...
African Journal of Biotechnology, Sep 5, 2007
NERICA rices are interspecific inbred progeny derived from crosses between Oryza sativa x O. glab... more NERICA rices are interspecific inbred progeny derived from crosses between Oryza sativa x O. glaberrima. In this study, we evaluated 70 BC 2 interspecific lines, developed by crossing a tropical japonica variety (WAB 56-104) as the recurrent parent to an O. glaberrima variety (CG 14) as the donor parent, followed by the use of anther culture to derive doubled haploids (DH) (26 lines) or eight generations of inbreeding to fix the lines (44 lines). Seven of these BC 2 derived inbred lines have been released as NERICA 1-NERICA 7. This study examined the relative contribution of each parent and the extent of genetic differences among these 70 sister lines using 130 well-distributed microsatellite markers which cover 1725 cM of the rice genome. The average proportion of O. sativa recurrent parent genome was 87.4% (1,508 cM), while the observed average proportion of O. glaberrima donor genome was 6.3% (108 cM). Non-parental alleles were detected in 83% of the lines and contributed an average of 38 cM per line (~2.2% of genomic DNA). Lines that had undergone eight generations of inbreeding in the field contained significantly more non-parental alleles (av. 2.7%) compared to the DH lines (av. 1.3%) that were developed from BC 2 anthers. Using both cluster and principal component analyses, two major groups were detected in these materials. The NERICA varieties (NERICA 1 to 7) clustered in one group while the remaining 63 lines clustered in another group, suggesting that the second group may offer significant opportunities for further selection and variety development.
AFRICAN JOURNAL OF AGRICULTURAL RESEEARCH, 2012
Two dry-season field experiments were conducted at AfricaRice research station in Benin to identi... more Two dry-season field experiments were conducted at AfricaRice research station in Benin to identify drought tolerant rice genotypes from a range of genetic resources: in 2006 using 202 backcross-inbred interspecific Oryza sativa Oryza glaberrima lines, replicated in 2007 (experiment 1); and in 2007 (replicated in 2008) using a population of 327 genotypes comprising O. glaberrima, O. sativa, interspecific lines and local landraces (experiment 2). Plots were fully irrigated from sowing to maturity (control) or subjected to 21-day drought (drought), respectively. Plant height, number of tillers and grain yield values were higher under control than drought for most genotypes. Contrary observations were made for leaf greenness (SPAD), leaf temperature, flowering and maturity. The 24 top-yielding lines in experiment 1 and 20 top-yielding lines in experiment 2 followed this general trend. Significant genotype environment interaction was observed for SPAD, number of tillers and grain yield. Grain yield, flowering and maturity were affected by drought for 98.0, 95.1 and 100% genotypes, respectively, for experiment 1, and 99.1, 99.4 and 98.2%, respectively, for experiment 2. The study identified 003-2-2, 77-2-4, 61-1-1, 94-1-5, 94-2-3, 117-2-6, 77-5-3 (interspecific lines), and TOG6383, TOG5691, RAM122, TOG5919 (O. glaberrima), as stable or high yielding genotypes under drought and potential resources for further drought studies.
Agriculture & Food Security, 2015
Background: Tillabéry is the main rice growing region of Niger, and it includes both irrigated an... more Background: Tillabéry is the main rice growing region of Niger, and it includes both irrigated and lowland rice. Rice production has stagnated due to several factors this research investigated through farmers' eyes. Methods: Semi-structured group discussions were carried out in 14 villages in which 153 farmers, after giving their informed consent, were individually subjected to a questionnaire, and farmers' fields and storage facilities were visited. Results: Fields were larger in private irrigation and lowland agrosystems compared to those in public irrigation schemes. The local farmers' union was the only formal seed dissemination system. Farmers exchanged seed as well as did re-seeding of leftovers from the previous harvest. They indicated Rice yellow mottle virus (RYMV) and bacterial leaf blight (BLB) as the most prevalent biotic stresses in the irrigated agrosystems, but the RYMV-susceptible cultivars IR1529 and 'Waihidjo' are still the most popular varieties. Floods, birds, and hippopotamuses were the most damaging agents in lowland agrosystems where the landrace 'Degaulle'/D5237 was the preferred cultivar. Conclusions: Rice farmers in the region of Tillabéry were aware of the RYMV, could provide good descriptions of its symptoms, but could not establish the real causes of the disease nor its relationship with insects' prevalence and other cultural practices. However, traditional management strategies were implemented to reduce RYMV epidemics. This situation showed that farmers in the region of Tillabéry were willing to face RYMV epidemic outbreaks while growing their preferred rice cultivars. Good seed availability and absence of seed policy at the time of this study were also detected as bottlenecks in rice production increase in Tillabéry.
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Papers by Marie Ndjiondjop